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Agent-based models have proven to be useful tools in supporting decision-making processes in different application domains. The advent of modern computers and supercomputers has enabled these bottom-up approaches to realistically model human mobility and contact behavior.

The COVID-19 pandemic showcased the urgent need for detailed and informative models that can answer research questions on transmission dynamics. We present a sophisticated agent-based model to simulate the spread of respiratory diseases. The model is highly modularized and can be used on various scales, from a small collection of buildings up to cities or countries. Although not being the focus of this paper, the model has undergone performance engineering on a single core and provides an efficient intra- and inter-simulation parallelization for time-critical decision-making processes.

In order to allow answering research questions on individual level resolution, nonpharmaceutical intervention strategies such as face masks or venue closures can be implemented for particular locations or agents. In particular, we allow for sophisticated testing and isolation strategies to study the effects of minimal-invasive infectious disease mitigation.

With realistic human mobility patterns for the region of Brunswick, Germany, we study the effects of different interventions between March 1st and May 30, 2021 in the SARS-CoV-2 pandemic. Our analyses suggest that symptom-independent testing has limited impact on the mitigation of disease dynamics if the dark figure in symptomatic cases is high. Furthermore, we found that quarantine length is more important than quarantine efficiency but that, with sufficient symptomatic control, also short quarantines can have a substantial effect.

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Acute kidney injury (AKI) is common in children with congenital heart disease following open-heart surgery with cardiopulmonary bypass (CPB). Early AKI detection in critically ill children requires clinician expertise to compile various data from different sources within a stressful and time-sensitive environment. However, as electronic health records provide data in a machine-readable format, this process could be supported by computerized systems. Therefore, we developed a time-aware, rule-based clinical decision support system (CDSS) to detect, stage, and track temporal AKI progression in children.

Nucleus segmentation is an important analysis task in digital pathology. However, methods for automatic segmentation often struggle with new data from a different distribution, requiring users to manually annotate nuclei and retrain data-specific models. Vision foundation models (VFMs), such as the Segment Anything Model (SAM), offer a more robust alternative for automatic and interactive segmentation. Despite their success in natural images, a foundation model for nucleus segmentation in histopathology is still missing. Initial efforts to adapt SAM have shown some success, but did not yet introduce a comprehensive model for diverse segmentation tasks. To close this gap, we introduce PathoSAM, a VFM for nucleus segmentation, based on training SAM on a diverse dataset. Our extensive experiments show that it is the new state-of-the-art model for automatic and interactive nucleus instance segmentation in histopathology. We also demonstrate how it can be adapted for other segmentation tasks, including semantic nucleus segmentation. For this task, we show that it yields results better than popular methods, while not yet beating the state-of-the-art, CellViT. Our models are open-source and compatible with popular tools for data annotation. We also provide scripts for whole-slide image segmentation.

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Segmentation is an important analysis task for biomedical images, enabling the study of individual organelles, cells or organs. Deep learning has massively improved segmentation methods, but challenges remain in generalization to new conditions, requiring costly data annotation. Vision foundation models, such as Segment Anything Model (SAM), address this issue through improved generalization. However, these models still require finetuning on annotated data, although with less annotations, to achieve optimal results for new conditions. As a downside, they require more computational resources. This makes parameter-efficient finetuning (PEFT) relevant. We contribute the first comprehensive study of PEFT for SAM applied to biomedical images. We find that the placement of PEFT layers is more important for efficiency than the type of layer for vision transformers and we provide a recipe for resource-efficient finetuning.

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An automatic classification of the malignancy of lung nodules in computed tomography (CT) scans can support early detection of lung cancer, which is crucial for the treatment success. The novel photon-counting CT (PCCT) technology enables high image quality with a low radiation dose and provides additional spectral information. This research focuses on whether PCCT scans offer a benefit in the automatic classification of lung nodules. Establishing a dataset of PCCT images poses several challenges, such as the extraction of annotations or the data imbalance.

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In the course of antibody affinity maturation, germinal centre (GC) B cells mutate their immunoglobulin heavy- and light-chain genes in a process known as somatic hypermutation (SHM). Panels of mutant B cells with different binding affinities for antigens are then selected in a Darwinian manner, which leads to a progressive increase in affinity among the population. As with any Darwinian process, rare gain-of-fitness mutations must be identified and common loss-of-fitness mutations avoided. Progressive acquisition of mutations therefore poses a risk during large proliferative bursts, when GC B cells undergo several cell cycles in the absence of affinity-based selection. Using a combination of in vivo mouse experiments and mathematical modelling, here we show that GCs achieve this balance by strongly suppressing SHM during clonal-burst-type expansion, so that a large fraction of the progeny generated by these bursts does not deviate from their ancestral genotype. Intravital imaging and image-based cell sorting of a mouse strain carrying a reporter of cyclin-dependent kinase 2 (CDK2) activity showed that B cells that are actively undergoing proliferative bursts lack the transient CDK2low ‘G0-like’ phase of the cell cycle in which SHM takes place. We propose a model in which inertially cycling B cells mostly delay SHM until the G0-like phase that follows their final round of division in the GC dark zone, thus maintaining affinity as they clonally expand in the absence of selection.